Report ligand ID & continue on batch ligand preparation error

[Billsfriend]

I was preparing batch ligand pdbqt using mk_prepare_ligand.py from scrub.py output sdf file, and I encountered an error:

Traceback (most recent call last):
  File "/home/gjsx/micromamba/envs/ringtail/bin/mk_prepare_ligand.py", line 10, in <module>
    sys.exit(main())
  File "/home/gjsx/micromamba/envs/ringtail/lib/python3.10/site-packages/meeko/cli/mk_prepare_ligand.py", line 613, in main
    molsetups = preparator.prepare(mol)
  File "/home/gjsx/micromamba/envs/ringtail/lib/python3.10/site-packages/meeko/preparation.py", line 489, in prepare
    setup = setup_class.from_mol(
  File "/home/gjsx/micromamba/envs/ringtail/lib/python3.10/site-packages/meeko/molsetup.py", line 1607, in from_mol
    raise ValueError(f"RDKit molecule has {len(Chem.GetMolFrags(mol))} fragments. Must have 1.")
ValueError: RDKit molecule has 2 fragments. Must have 1.

The reason was clear, but I did not get to know which SMILES and ligand ID caused this error in my ligand batch.
It will be helpful if the SMILES and ID are printed like warnings I got from mk_prepare_ligand.py:

warning: found the maximum nr of matches (17) in RDKitMolSetup.get_symmetries_for_rmsd
Maybe this molecule is "too" symmetric? ZINC000001667248 CC(C)(c1ccccc1)C(C)(C)c1ccccc1

Also, it will be better if we can treat fragment error as a warning and continue to prepare other ligands in batch mode.

[diogomart]

Will do.